The man had apparently not been overseas, a health ministry official said. Other details were not immediately available.
The H1N1 flu outbreak, declared a pandemic in June, has spread around the world and could eventually affect 2 billion people, according to World Health Organisation estimates.
Japan had confirmed some 5,000 cases of the disease as of last month, when it stopped keeping track. The virus has killed more than 800 people worldwide since April.
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